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From: David C. <dc...@ma...> - 2008-10-16 11:29:33
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Hi All, There's an example PMF file here: http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? David -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Jones, A. <And...@li...> - 2008-10-16 12:37:13
|
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 16 October 2008 12:29
> To: psi...@li...
> Subject: [Psidev-pi-dev] AnalysisXML PMF Example
>
> Hi All,
>
> There's an example PMF file here:
>
> http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml
>
> The only small problem that I can see is that for
> <SpectrumIdentificationItem>
>
> the schema has:
> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
> maxOccurs="unbounded"/>
> <xsd:element ref="pf:Param" maxOccurs="unbounded"/>
>
> and I can't think of any required CV here
>
> To find it, search for
> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
> to say here here"
>
> I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees?
>
> David
>
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
>
> dc...@ma...
> http://www.matrixscience.com
>
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
|
|
From: David C. <dc...@ma...> - 2008-10-16 12:53:46
|
Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: > Hi David, > > You may be right that the parameter should be optionally anyway, but in this > particular example is there not some score assigned to the peptide-spectrum > identification? > > In the equivalent MS/MS example, we have: > > <pf:cvParam accession="PI:00171" name="mascot:score" > cvRef="PSI-PI" value="62.72" /> > <pf:cvParam accession="PI:00172" name="mascot:expectation value" > cvRef="PSI-PI" value="0.000863428353297988" /> > <pf:cvParam accession="PI:99999" name="mascot_rank" > cvRef="PSI-PI" value="1" /> > > Are the same sort of scores not valid for PMF as well...? > > Cheers > Andy > > >> -----Original Message----- >> From: David Creasy [mailto:dc...@ma...] >> Sent: 16 October 2008 12:29 >> To: psi...@li... >> Subject: [Psidev-pi-dev] AnalysisXML PMF Example >> >> Hi All, >> >> There's an example PMF file here: >> >> http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml >> >> The only small problem that I can see is that for >> <SpectrumIdentificationItem> >> >> the schema has: >> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" >> maxOccurs="unbounded"/> >> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> >> >> and I can't think of any required CV here >> >> To find it, search for >> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt >> to say here here" >> >> I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? >> >> David >> >> -- >> David Creasy >> Matrix Science >> 64 Baker Street >> London W1U 7GB, UK >> Tel: +44 (0)20 7486 1050 >> Fax: +44 (0)20 7224 1344 >> >> dc...@ma... >> http://www.matrixscience.com >> >> Matrix Science Ltd. is registered in England and Wales >> Company number 3533898 >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Jones, A. <And...@li...> - 2008-10-16 13:05:45
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Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 16 October 2008 13:54 > To: psi...@li... > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > Hi Andy, > > For PMF, with Mascot, (and all other search engines as far as I know), > there is no score assigned to matching a single peak to an individual > peptide. A score for one peak in isolation would have little meaning - > you can only really score the match of the complete spectrum. > > David > > Jones, Andy wrote: > > Hi David, > > > > You may be right that the parameter should be optionally anyway, but in this > > particular example is there not some score assigned to the peptide-spectrum > > identification? > > > > In the equivalent MS/MS example, we have: > > > > <pf:cvParam accession="PI:00171" name="mascot:score" > > cvRef="PSI-PI" value="62.72" /> > > <pf:cvParam accession="PI:00172" name="mascot:expectation value" > > cvRef="PSI-PI" value="0.000863428353297988" /> > > <pf:cvParam accession="PI:99999" name="mascot_rank" > > cvRef="PSI-PI" value="1" /> > > > > Are the same sort of scores not valid for PMF as well...? > > > > Cheers > > Andy > > > > > >> -----Original Message----- > >> From: David Creasy [mailto:dc...@ma...] > >> Sent: 16 October 2008 12:29 > >> To: psi...@li... > >> Subject: [Psidev-pi-dev] AnalysisXML PMF Example > >> > >> Hi All, > >> > >> There's an example PMF file here: > >> > >> http://code.google.com/p/psi- > pi/source/browse/trunk/examples/PMF_example.axml > >> > >> The only small problem that I can see is that for > >> <SpectrumIdentificationItem> > >> > >> the schema has: > >> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" > >> maxOccurs="unbounded"/> > >> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> > >> > >> and I can't think of any required CV here > >> > >> To find it, search for > >> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt > >> to say here here" > >> > >> I suggest that we have minOccurs=0 for pfParam here unless anyone > disagrees? > >> > >> David > >> > >> -- > >> David Creasy > >> Matrix Science > >> 64 Baker Street > >> London W1U 7GB, UK > >> Tel: +44 (0)20 7486 1050 > >> Fax: +44 (0)20 7224 1344 > >> > >> dc...@ma... > >> http://www.matrixscience.com > >> > >> Matrix Science Ltd. is registered in England and Wales > >> Company number 3533898 > >> > >> > >> ------------------------------------------------------------------------- > >> This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > >> Build the coolest Linux based applications with Moblin SDK & win great prizes > >> Grand prize is a trip for two to an Open Source event anywhere in the world > >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ > >> _______________________________________________ > >> Psidev-pi-dev mailing list > >> Psi...@li... > >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > > Build the coolest Linux based applications with Moblin SDK & win great prizes > > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Pierre-Alain B. <pie...@is...> - 2008-10-16 13:24:27
|
Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: > Ah, I was getting confused, I was thinking that there would be one > SpectrumIdentificationItem for one Spectrum, in fact there is one for each > peptide. > > The problem with the way it's encoded (probably the only way possible without a > schema change) is that it's not obvious how to tie together all the results from > a single spectrum-protein identification. Even querying for the same spectrumID > will not resolve it, since there may be multiple ranked spectrum-protein > identifications from the same spectrum. > > I suggest we look at this in the call, I think we might need an alteration to > the schema to model PMF more intuitively, unless I've misunderstood something. > > Cheers > Andy > > > > > > >> -----Original Message----- >> From: David Creasy [mailto:dc...@ma...] >> Sent: 16 October 2008 13:54 >> To: psi...@li... >> Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example >> >> Hi Andy, >> >> For PMF, with Mascot, (and all other search engines as far as I know), >> there is no score assigned to matching a single peak to an individual >> peptide. A score for one peak in isolation would have little meaning - >> you can only really score the match of the complete spectrum. >> >> David >> >> Jones, Andy wrote: >> >>> Hi David, >>> >>> You may be right that the parameter should be optionally anyway, but in this >>> particular example is there not some score assigned to the peptide-spectrum >>> identification? >>> >>> In the equivalent MS/MS example, we have: >>> >>> <pf:cvParam accession="PI:00171" name="mascot:score" >>> cvRef="PSI-PI" value="62.72" /> >>> <pf:cvParam accession="PI:00172" name="mascot:expectation value" >>> cvRef="PSI-PI" value="0.000863428353297988" /> >>> <pf:cvParam accession="PI:99999" name="mascot_rank" >>> cvRef="PSI-PI" value="1" /> >>> >>> Are the same sort of scores not valid for PMF as well...? >>> >>> Cheers >>> Andy >>> >>> >>> >>>> -----Original Message----- >>>> From: David Creasy [mailto:dc...@ma...] >>>> Sent: 16 October 2008 12:29 >>>> To: psi...@li... >>>> Subject: [Psidev-pi-dev] AnalysisXML PMF Example >>>> >>>> Hi All, >>>> >>>> There's an example PMF file here: >>>> >>>> http://code.google.com/p/psi- >>>> >> pi/source/browse/trunk/examples/PMF_example.axml >> >>>> The only small problem that I can see is that for >>>> <SpectrumIdentificationItem> >>>> >>>> the schema has: >>>> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" >>>> maxOccurs="unbounded"/> >>>> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> >>>> >>>> and I can't think of any required CV here >>>> >>>> To find it, search for >>>> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt >>>> to say here here" >>>> >>>> I suggest that we have minOccurs=0 for pfParam here unless anyone >>>> >> disagrees? >> >>>> David >>>> >>>> -- >>>> David Creasy >>>> Matrix Science >>>> 64 Baker Street >>>> London W1U 7GB, UK >>>> Tel: +44 (0)20 7486 1050 >>>> Fax: +44 (0)20 7224 1344 >>>> >>>> dc...@ma... >>>> http://www.matrixscience.com >>>> >>>> Matrix Science Ltd. is registered in England and Wales >>>> Company number 3533898 >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> This SF.Net email is sponsored by the Moblin Your Move Developer's >>>> >> challenge >> >>>> Build the coolest Linux based applications with Moblin SDK & win great >>>> > prizes > >>>> Grand prize is a trip for two to an Open Source event anywhere in the world >>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>> _______________________________________________ >>>> Psidev-pi-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >>>> >>> ------------------------------------------------------------------------- >>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >>> Build the coolest Linux based applications with Moblin SDK & win great >>> > prizes > >>> Grand prize is a trip for two to an Open Source event anywhere in the world >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>> _______________________________________________ >>> Psidev-pi-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >>> >> -- >> David Creasy >> Matrix Science >> 64 Baker Street >> London W1U 7GB, UK >> Tel: +44 (0)20 7486 1050 >> Fax: +44 (0)20 7224 1344 >> >> dc...@ma... >> http://www.matrixscience.com >> >> Matrix Science Ltd. is registered in England and Wales >> Company number 3533898 >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > |
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From: Jones, A. <And...@li...> - 2008-10-16 16:26:43
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New schema uploaded by SVN with changes agreed on the call: - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data) - Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification - Altered documentation for SpectrumIdentificationResult – one SpectrumIdentificationResult for one spectrum - Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique, removed SpectrumElement Andy From: Pierre-Alain Binz [mailto:pie...@is...] Sent: 16 October 2008 14:26 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 13:54 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: Hi David, You may be right that the parameter should be optionally anyway, but in this particular example is there not some score assigned to the peptide-spectrum identification? In the equivalent MS/MS example, we have: <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="62.72" /> <pf:cvParam accession="PI:00172" name="mascot:expectation value" cvRef="PSI-PI" value="0.000863428353297988" /> <pf:cvParam accession="PI:99999" name="mascot_rank" cvRef="PSI-PI" value="1" /> Are the same sort of scores not valid for PMF as well...? Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 12:29 To: psi...@li... Subject: [Psidev-pi-dev] AnalysisXML PMF Example Hi All, There's an example PMF file here: http://code.google.com/p/psi- pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? David -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Jones, A. <And...@li...> - 2008-10-17 12:17:16
|
A few more minor schema changes – no changes to instance docs needed: - Generally added bits of documentation after reviewing the autogenerated docs from Eric - Changed the data type on MassTable-residue from xsd:string to a single character A-Z, seem reasonable? - Added some docs to FuGElight There is another change I want to make which won’t affect any current instances but does place an extra restriction. Currently AnalysisCollection references pf:ProtocolApplication and AnalysisProtocolCollection references pf:Protocol, so any subclasses of these can be used – including FuGE GenericProtocol and GenericProtocolApplication (which we don’t want to support in version 1). We also have an abstract AnalysisProtocol and AnalysisProtocolApplication in the schema which we aren’t using. I would like to remove all the attributes from AnalysisProtocol and AnalysisProtocolApplication, just leaving documentation explaining that this is an extension point from which new Protocols or ProtocolApplications will be added in later versions. AnalysisCollection would then reference AnalysisProtocolApplication, of which the only available subclasses are SpectrumIdentification and ProteinDetection (new analyses may be added in v 2) and AnalysisProtocolCollection would reference AnalysisProtocol. This won’t affect current instances but is a reasonable structural change so I wanted to circulate it to the list before I make this change – if I don’t hear any dissent I’ll change this. Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 16 October 2008 17:26 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example New schema uploaded by SVN with changes agreed on the call: - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data) - Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification - Altered documentation for SpectrumIdentificationResult – one SpectrumIdentificationResult for one spectrum - Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique, removed SpectrumElement Andy From: Pierre-Alain Binz [mailto:pie...@is...] Sent: 16 October 2008 14:26 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 13:54 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: Hi David, You may be right that the parameter should be optionally anyway, but in this particular example is there not some score assigned to the peptide-spectrum identification? In the equivalent MS/MS example, we have: <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="62.72" /> <pf:cvParam accession="PI:00172" name="mascot:expectation value" cvRef="PSI-PI" value="0.000863428353297988" /> <pf:cvParam accession="PI:99999" name="mascot_rank" cvRef="PSI-PI" value="1" /> Are the same sort of scores not valid for PMF as well...? Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 12:29 To: psi...@li... Subject: [Psidev-pi-dev] AnalysisXML PMF Example Hi All, There's an example PMF file here: http://code.google.com/p/psi- pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? David -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
|
From: Jones, A. <And...@li...> - 2008-10-17 14:42:57
|
Another minor schema update: added Key KeyRef for Measures within FragmentArray.
The FragmentationTable was missing from the Mascot example (sorry David!). Here
is what it should look like:
<SpectrumIdentificationList id="SIL_1" numSequencesSearched="71412">
<FragmentationTable>
<Measure id="m_mz">
<pf:cvParam cvRef="PSI-PI" accession="PI:00225" name="product ion
m/z"/>
</Measure>
<Measure id="m_intensity">
<pf:cvParam cvRef="PSI-PI" accession="PI:00226" name="product ion
intensity"/>
</Measure>
</FragmentationTable>
Also made a few minor additions to the spec doc.
Cheers
Andy
From: Jones, Andy [mailto:And...@li...]
Sent: 17 October 2008 13:17
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
A few more minor schema changes – no changes to instance docs needed:
- Generally added bits of documentation after reviewing the
autogenerated docs from Eric
- Changed the data type on MassTable-residue from xsd:string to a
single character A-Z, seem reasonable?
- Added some docs to FuGElight
There is another change I want to make which won’t affect any current instances
but does place an extra restriction.
Currently AnalysisCollection references pf:ProtocolApplication and
AnalysisProtocolCollection references pf:Protocol, so any subclasses of these
can be used – including FuGE GenericProtocol and GenericProtocolApplication
(which we don’t want to support in version 1).
We also have an abstract AnalysisProtocol and AnalysisProtocolApplication in the
schema which we aren’t using. I would like to remove all the attributes from
AnalysisProtocol and AnalysisProtocolApplication, just leaving documentation
explaining that this is an extension point from which new Protocols or
ProtocolApplications will be added in later versions.
AnalysisCollection would then reference AnalysisProtocolApplication, of which
the only available subclasses are SpectrumIdentification and ProteinDetection
(new analyses may be added in v 2) and AnalysisProtocolCollection would
reference AnalysisProtocol.
This won’t affect current instances but is a reasonable structural change so I
wanted to circulate it to the list before I make this change – if I don’t hear
any dissent I’ll change this.
Cheers
Andy
From: Jones, Andy [mailto:And...@li...]
Sent: 16 October 2008 17:26
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a
single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult – one
SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of
SpectrumIdentificationResult, and made these composite unique, removed
SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple,
similar to "weights" that coulld be attributed to a specific fragment ion match
in a MS/MS spectrum. But at the end, even if a software goes through this, and
maybe scores the peptides in an intermediary process, it will at the end always
link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s)
is(are) proteins). It can annotate the spectrum, either with potential peptides
of fragments, respectively. Anyway, we have not encoded any scores to the
interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it
for PMF. Annotation is the sole point of discussion, which I think we want to
postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway,
but in this
particular example is there not some score assigned to the
peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172"
name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence"
minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required
content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here
unless anyone
disagrees?
David
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move
Developer's
challenge
Build the coolest Linux based applications with Moblin
SDK & win great
prizes
Grand prize is a trip for two to an Open Source event
anywhere in the world
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_______________________________________________
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Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move
Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win
great
prizes
Grand prize is a trip for two to an Open Source event anywhere
in the world
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_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the
world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
|
|
From: David C. <dc...@ma...> - 2008-10-17 15:10:22
|
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<meta content="text/html;charset=windows-1252"
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</head>
<body bgcolor="#ffffff" text="#000000">
Ah yes... fixed now.<br>
(The examples don't contain real fragment masses yet - I'm just working
on this now).<br>
<br>
David<br>
<br>
Jones, Andy wrote:
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<div class="Section1">
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Another
minor schema update: added Key KeyRef for Measures
within FragmentArray.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">The
FragmentationTable was missing from the Mascot example
(sorry David!). Here is what it should look like:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">
<SpectrumIdentificationList id="SIL_1"
numSequencesSearched="71412"><br>
<FragmentationTable><br>
<Measure id="m_mz"><br>
<pf:cvParam cvRef="PSI-PI" accession="PI:00225"
name="product ion m/z"/><br>
</Measure><br>
<Measure id="m_intensity"><br>
<pf:cvParam cvRef="PSI-PI" accession="PI:00226"
name="product ion intensity"/><br>
</Measure> <br>
</FragmentationTable><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Also
made a few minor additions to the spec doc.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b>Sent:</b> 17 October 2008 13:17<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">A
few more minor schema changes – no changes to instance docs
needed:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Generally
added bits of documentation after reviewing the
autogenerated docs from Eric<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Changed
the data type on MassTable-residue from xsd:string to a
single character A-Z, seem reasonable?<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Added
some docs to FuGElight<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">There
is another change I want to make which won’t affect any
current instances but does place an extra restriction.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Currently
AnalysisCollection references pf:ProtocolApplication
and AnalysisProtocolCollection references pf:Protocol, so any
subclasses of
these can be used – including FuGE GenericProtocol and
GenericProtocolApplication (which we don’t want to support in version
1). <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">We
also have an abstract AnalysisProtocol and
AnalysisProtocolApplication in the schema which we aren’t using. I
would like
to remove all the attributes from AnalysisProtocol and
AnalysisProtocolApplication, just leaving documentation explaining that
this is
an extension point from which new Protocols or ProtocolApplications
will be
added in later versions.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">AnalysisCollection
would then reference
AnalysisProtocolApplication, of which the only available subclasses are
SpectrumIdentification and ProteinDetection (new analyses may be added
in v 2) and
AnalysisProtocolCollection would reference AnalysisProtocol.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">This
won’t affect current instances but is a reasonable
structural change so I wanted to circulate it to the list before I make
this
change – if I don’t hear any dissent I’ll change this.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b>Sent:</b> 16 October 2008 17:26<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">New
schema uploaded by SVN with changes agreed on the call:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to
handle PMF data)<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Altered documentation for SpectrumIdentificationItem to
clarify that this is a single peptide-spectrum identification<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Altered documentation for SpectrumIdentificationResult – one
SpectrumIdentificationResult for one spectrum<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Moved spectrumID and SpectraData_ref as attributes of
SpectrumIdentificationResult, and made these composite unique, removed
SpectrumElement<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Pierre-Alain Binz [<a class="moz-txt-link-freetext" href="mailto:pie...@is...">mailto:pie...@is...</a>] <br>
<b>Sent:</b> 16 October 2008 14:26<br>
<b>To:</b> Jones, Andy<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Actually, there might be a score associated with
each
peptide - peak couple, similar to "weights" that coulld be attributed
to a specific fragment ion match in a MS/MS spectrum. But at the end,
even if a
software goes through this, and maybe scores the peptides in an
intermediary
process, it will at the end always link a spectrum with one or more
molecule(s)
(in the case of PMF the molecule(s) is(are) proteins). It can annotate
the
spectrum, either with potential peptides of fragments, respectively.
Anyway, we
have not encoded any scores to the interpretation of fragment ions in
MS/MS
spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole
point of
discussion, which I think we want to postone for v2, right?<br>
<br>
<br>
Pierre-Alain<br>
<br>
Jones, Andy wrote: <o:p></o:p></p>
<pre>Ah, I was getting confused, I was thinking that there would be one<o:p></o:p></pre>
<pre>SpectrumIdentificationItem for one Spectrum, in fact there is one for each<o:p></o:p></pre>
<pre>peptide.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>The problem with the way it's encoded (probably the only way possible without a<o:p></o:p></pre>
<pre>schema change) is that it's not obvious how to tie together all the results from<o:p></o:p></pre>
<pre>a single spectrum-protein identification. Even querying for the same spectrumID<o:p></o:p></pre>
<pre>will not resolve it, since there may be multiple ranked spectrum-protein<o:p></o:p></pre>
<pre>identifications from the same spectrum.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I suggest we look at this in the call, I think we might need an alteration to<o:p></o:p></pre>
<pre>the schema to model PMF more intuitively, unless I've misunderstood something.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers<o:p></o:p></pre>
<pre>Andy<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: David Creasy [<a moz-do-not-send="true"
href="mailto:dc...@ma...">mailto:dc...@ma...</a>]<o:p></o:p></pre>
<pre>Sent: 16 October 2008 13:54<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><o:p></o:p></pre>
<pre>Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi Andy,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>For PMF, with Mascot, (and all other search engines as far as I know),<o:p></o:p></pre>
<pre>there is no score assigned to matching a single peak to an individual<o:p></o:p></pre>
<pre>peptide. A score for one peak in isolation would have little meaning -<o:p></o:p></pre>
<pre>you can only really score the match of the complete spectrum.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>David<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Jones, Andy wrote:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Hi David,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>You may be right that the parameter should be optionally anyway, but in this<o:p></o:p></pre>
<pre>particular example is there not some score assigned to the peptide-spectrum<o:p></o:p></pre>
<pre>identification?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>In the equivalent MS/MS example, we have:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <pf:cvParam accession="PI:00171" name="mascot:score"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="62.72" /><o:p></o:p></pre>
<pre> <pf:cvParam accession="PI:00172" name="mascot:expectation value"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="0.000863428353297988" /><o:p></o:p></pre>
<pre> <pf:cvParam accession="PI:99999" name="mascot_rank"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="1" /><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Are the same sort of scores not valid for PMF as well...?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers<o:p></o:p></pre>
<pre>Andy<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: David Creasy [<a moz-do-not-send="true"
href="mailto:dc...@ma...">mailto:dc...@ma...</a>]<o:p></o:p></pre>
<pre>Sent: 16 October 2008 12:29<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><o:p></o:p></pre>
<pre>Subject: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi All,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>There's an example PMF file here:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a moz-do-not-send="true"
href="http://code.google.com/p/psi">http://code.google.com/p/psi</a>-<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>pi/source/browse/trunk/examples/PMF_example.axml<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>The only small problem that I can see is that for<o:p></o:p></pre>
<pre> <SpectrumIdentificationItem><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>the schema has:<o:p></o:p></pre>
<pre> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"<o:p></o:p></pre>
<pre>maxOccurs="unbounded"/><o:p></o:p></pre>
<pre> <xsd:element ref="pf:Param" maxOccurs="unbounded"/><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>and I can't think of any required CV here<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>To find it, search for<o:p></o:p></pre>
<pre><pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt<o:p></o:p></pre>
<pre>to say here here"<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I suggest that we have minOccurs=0 for pfParam here unless anyone<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>disagrees?<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>David<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>--<o:p></o:p></pre>
<pre>David Creasy<o:p></o:p></pre>
<pre>Matrix Science<o:p></o:p></pre>
<pre>64 Baker Street<o:p></o:p></pre>
<pre>London W1U 7GB, UK<o:p></o:p></pre>
<pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre>
<pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:dc...@ma...">dc...@ma...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://www.matrixscience.com">http://www.matrixscience.com</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Matrix Science Ltd. is registered in England and Wales<o:p></o:p></pre>
<pre>Company number 3533898<o:p></o:p></pre>
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<pre>This SF.Net email is sponsored by the Moblin Your Move Developer's<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>challenge<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Build the coolest Linux based applications with Moblin SDK & win great<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
</blockquote>
<pre>prizes<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Grand prize is a trip for two to an Open Source event anywhere in the world<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
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<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
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</blockquote>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
<pre>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge<o:p></o:p></pre>
<pre>Build the coolest Linux based applications with Moblin SDK & win great<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>prizes<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Grand prize is a trip for two to an Open Source event anywhere in the world<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
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href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
<pre>--<o:p></o:p></pre>
<pre>David Creasy<o:p></o:p></pre>
<pre>Matrix Science<o:p></o:p></pre>
<pre>64 Baker Street<o:p></o:p></pre>
<pre>London W1U 7GB, UK<o:p></o:p></pre>
<pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre>
<pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:dc...@ma...">dc...@ma...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://www.matrixscience.com">http://www.matrixscience.com</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Matrix Science Ltd. is registered in England and Wales<o:p></o:p></pre>
<pre>Company number 3533898<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
<pre>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge<o:p></o:p></pre>
<pre>Build the coolest Linux based applications with Moblin SDK & win great prizes<o:p></o:p></pre>
<pre>Grand prize is a trip for two to an Open Source event anywhere in the world<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
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From: David C. <dc...@ma...> - 2008-10-17 12:40:38
|
I've updated the four Mascot MSMS examples and the PMF example as discussed in the call. Is the PMF example any clearer now? http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml Corresponding Mascot report can be seen here: http://www.matrixscience.com/cgi/master_results.pl?file=../data/F981122.dat For the MS-MS, I wonder if we should have 'rank' as an attribute for <SpectrumIdentificationItem> rather than using CV since I think it will be common across all search engines? (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment). David Jones, Andy wrote: > New schema uploaded by SVN with changes agreed on the call: > > > > > > - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle > PMF data) > > - Altered documentation for SpectrumIdentificationItem to clarify that > this is a single peptide-spectrum identification > > - Altered documentation for SpectrumIdentificationResult – one > SpectrumIdentificationResult for one spectrum > > - Moved spectrumID and SpectraData_ref as attributes of > SpectrumIdentificationResult, and made these composite unique, removed > SpectrumElement > > > > > > Andy > > > > > > *From:* Pierre-Alain Binz [mailto:pie...@is...] > *Sent:* 16 October 2008 14:26 > *To:* Jones, Andy > *Cc:* psi...@li... > *Subject:* Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > Actually, there might be a score associated with each peptide - peak > couple, similar to "weights" that coulld be attributed to a specific > fragment ion match in a MS/MS spectrum. But at the end, even if a > software goes through this, and maybe scores the peptides in an > intermediary process, it will at the end always link a spectrum with one > or more molecule(s) (in the case of PMF the molecule(s) is(are) > proteins). It can annotate the spectrum, either with potential peptides > of fragments, respectively. Anyway, we have not encoded any scores to > the interpretation of fragment ions in MS/MS spectra. Similarly, we > wouldn't do it for PMF. Annotation is the sole point of discussion, > which I think we want to postone for v2, right? > > > Pierre-Alain > > Jones, Andy wrote: > > Ah, I was getting confused, I was thinking that there would be one > > SpectrumIdentificationItem for one Spectrum, in fact there is one for each > > peptide. > > > > The problem with the way it's encoded (probably the only way possible without a > > schema change) is that it's not obvious how to tie together all the results from > > a single spectrum-protein identification. Even querying for the same spectrumID > > will not resolve it, since there may be multiple ranked spectrum-protein > > identifications from the same spectrum. > > > > I suggest we look at this in the call, I think we might need an alteration to > > the schema to model PMF more intuitively, unless I've misunderstood something. > > > > Cheers > > Andy > > > > > > > > > > > > > > -----Original Message----- > > From: David Creasy [mailto:dc...@ma...] > > Sent: 16 October 2008 13:54 > > To: psi...@li... <mailto:psi...@li...> > > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > Hi Andy, > > > > For PMF, with Mascot, (and all other search engines as far as I know), > > there is no score assigned to matching a single peak to an individual > > peptide. A score for one peak in isolation would have little meaning - > > you can only really score the match of the complete spectrum. > > > > David > > > > Jones, Andy wrote: > > > > Hi David, > > > > You may be right that the parameter should be optionally anyway, but in this > > particular example is there not some score assigned to the peptide-spectrum > > identification? > > > > In the equivalent MS/MS example, we have: > > > > <pf:cvParam accession="PI:00171" name="mascot:score" > > cvRef="PSI-PI" value="62.72" /> > > <pf:cvParam accession="PI:00172" name="mascot:expectation value" > > cvRef="PSI-PI" value="0.000863428353297988" /> > > <pf:cvParam accession="PI:99999" name="mascot_rank" > > cvRef="PSI-PI" value="1" /> > > > > Are the same sort of scores not valid for PMF as well...? > > > > Cheers > > Andy > > > > > > > > -----Original Message----- > > From: David Creasy [mailto:dc...@ma...] > > Sent: 16 October 2008 12:29 > > To: psi...@li... <mailto:psi...@li...> > > Subject: [Psidev-pi-dev] AnalysisXML PMF Example > > > > Hi All, > > > > There's an example PMF file here: > > > > http://code.google.com/p/psi- > > > > pi/source/browse/trunk/examples/PMF_example.axml > > > > The only small problem that I can see is that for > > <SpectrumIdentificationItem> > > > > the schema has: > > <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" > > maxOccurs="unbounded"/> > > <xsd:element ref="pf:Param" maxOccurs="unbounded"/> > > > > and I can't think of any required CV here > > > > To find it, search for > > <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt > > to say here here" > > > > I suggest that we have minOccurs=0 for pfParam here unless anyone > > > > disagrees? > > > > David > > > > -- > > David Creasy > > Matrix Science > > 64 Baker Street > > London W1U 7GB, UK > > Tel: +44 (0)20 7486 1050 > > Fax: +44 (0)20 7224 1344 > > > > dc...@ma... <mailto:dc...@ma...> > > http://www.matrixscience.com > > > > Matrix Science Ltd. is registered in England and Wales > > Company number 3533898 > > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's > > > > challenge > > > > Build the coolest Linux based applications with Moblin SDK & win great > > > > prizes > > > > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > > Build the coolest Linux based applications with Moblin SDK & win great > > > > prizes > > > > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > -- > > David Creasy > > Matrix Science > > 64 Baker Street > > London W1U 7GB, UK > > Tel: +44 (0)20 7486 1050 > > Fax: +44 (0)20 7224 1344 > > > > dc...@ma... <mailto:dc...@ma...> > > http://www.matrixscience.com > > > > Matrix Science Ltd. is registered in England and Wales > > Company number 3533898 > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > > Build the coolest Linux based applications with Moblin SDK & win great prizes > > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > > Build the coolest Linux based applications with Moblin SDK & win great prizes > > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: Jones, A. <And...@li...> - 2008-10-17 12:30:51
|
> Is the PMF example any clearer now? > http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml Looks good to me now. I think there's a chance that people may find the way results are separated into SpectrumIdentificationItems and ProteinHypotheses slightly confusing since the separation makes less sense for PMF than MS/MS but we probably have to live with this if we want to re-use the same general model structures. > For the MS-MS, I wonder if we should have 'rank' as an attribute for > <SpectrumIdentificationItem> rather than using CV since I think it will > be common across all search engines? > (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment). I'm in favour of this change, although it would have to be an optional attribute (and well documented) since it makes no sense for PMF data. Cheers Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 17 October 2008 12:53 > To: Jones, Andy > Cc: psi...@li... > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > I've updated the four Mascot MSMS examples and the PMF example as > discussed in the call. > > Is the PMF example any clearer now? > http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml > > Corresponding Mascot report can be seen here: > http://www.matrixscience.com/cgi/master_results.pl?file=../data/F981122.dat > > For the MS-MS, I wonder if we should have 'rank' as an attribute for > <SpectrumIdentificationItem> rather than using CV since I think it will > be common across all search engines? > (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment). > > David > > Jones, Andy wrote: > > New schema uploaded by SVN with changes agreed on the call: > > > > > > > > > > > > - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle > > PMF data) > > > > - Altered documentation for SpectrumIdentificationItem to clarify that > > this is a single peptide-spectrum identification > > > > - Altered documentation for SpectrumIdentificationResult – one > > SpectrumIdentificationResult for one spectrum > > > > - Moved spectrumID and SpectraData_ref as attributes of > > SpectrumIdentificationResult, and made these composite unique, removed > > SpectrumElement > > > > > > > > > > > > Andy > > > > > > > > > > > > *From:* Pierre-Alain Binz [mailto:pie...@is...] > > *Sent:* 16 October 2008 14:26 > > *To:* Jones, Andy > > *Cc:* psi...@li... > > *Subject:* Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > > > > > Actually, there might be a score associated with each peptide - peak > > couple, similar to "weights" that coulld be attributed to a specific > > fragment ion match in a MS/MS spectrum. But at the end, even if a > > software goes through this, and maybe scores the peptides in an > > intermediary process, it will at the end always link a spectrum with one > > or more molecule(s) (in the case of PMF the molecule(s) is(are) > > proteins). It can annotate the spectrum, either with potential peptides > > of fragments, respectively. Anyway, we have not encoded any scores to > > the interpretation of fragment ions in MS/MS spectra. Similarly, we > > wouldn't do it for PMF. Annotation is the sole point of discussion, > > which I think we want to postone for v2, right? > > > > > > Pierre-Alain > > > > Jones, Andy wrote: > > > > Ah, I was getting confused, I was thinking that there would be one > > > > SpectrumIdentificationItem for one Spectrum, in fact there is one for each > > > > peptide. > > > > > > > > The problem with the way it's encoded (probably the only way possible without a > > > > schema change) is that it's not obvious how to tie together all the results from > > > > a single spectrum-protein identification. Even querying for the same spectrumID > > > > will not resolve it, since there may be multiple ranked spectrum-protein > > > > identifications from the same spectrum. > > > > > > > > I suggest we look at this in the call, I think we might need an alteration to > > > > the schema to model PMF more intuitively, unless I've misunderstood > something. > > > > > > > > Cheers > > > > Andy > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: David Creasy [mailto:dc...@ma...] > > > > Sent: 16 October 2008 13:54 > > > > To: psi...@li... <mailto:psidev-pi- > de...@li...> > > > > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > > > > > Hi Andy, > > > > > > > > For PMF, with Mascot, (and all other search engines as far as I know), > > > > there is no score assigned to matching a single peak to an individual > > > > peptide. A score for one peak in isolation would have little meaning - > > > > you can only really score the match of the complete spectrum. > > > > > > > > David > > > > > > > > Jones, Andy wrote: > > > > > > > > Hi David, > > > > > > > > You may be right that the parameter should be optionally anyway, but in this > > > > particular example is there not some score assigned to the peptide- > spectrum > > > > identification? > > > > > > > > In the equivalent MS/MS example, we have: > > > > > > > > <pf:cvParam accession="PI:00171" name="mascot:score" > > > > cvRef="PSI-PI" value="62.72" /> > > > > <pf:cvParam accession="PI:00172" name="mascot:expectation > value" > > > > cvRef="PSI-PI" value="0.000863428353297988" /> > > > > <pf:cvParam accession="PI:99999" name="mascot_rank" > > > > cvRef="PSI-PI" value="1" /> > > > > > > > > Are the same sort of scores not valid for PMF as well...? > > > > > > > > Cheers > > > > Andy > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: David Creasy [mailto:dc...@ma...] > > > > Sent: 16 October 2008 12:29 > > > > To: psi...@li... <mailto:psidev-pi- > de...@li...> > > > > Subject: [Psidev-pi-dev] AnalysisXML PMF Example > > > > > > > > Hi All, > > > > > > > > There's an example PMF file here: > > > > > > > > http://code.google.com/p/psi- > > > > > > > > pi/source/browse/trunk/examples/PMF_example.axml > > > > > > > > The only small problem that I can see is that for > > > > <SpectrumIdentificationItem> > > > > > > > > the schema has: > > > > <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" > > > > maxOccurs="unbounded"/> > > > > <xsd:element ref="pf:Param" maxOccurs="unbounded"/> > > > > > > > > and I can't think of any required CV here > > > > > > > > To find it, search for > > > > <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but > nowt > > > > to say here here" > > > > > > > > I suggest that we have minOccurs=0 for pfParam here unless anyone > > > > > > > > disagrees? > > > > > > > > David > > > > > > > > -- > > > > David Creasy > > > > Matrix Science > > > > 64 Baker Street > > > > London W1U 7GB, UK > > > > Tel: +44 (0)20 7486 1050 > > > > Fax: +44 (0)20 7224 1344 > > > > > > > > dc...@ma... <mailto:dc...@ma...> > > > > http://www.matrixscience.com > > > > > > > > Matrix Science Ltd. is registered in England and Wales > > > > Company number 3533898 > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.Net email is sponsored by the Moblin Your Move Developer's > > > > > > > > challenge > > > > > > > > Build the coolest Linux based applications with Moblin SDK & win great > > > > > > > > prizes > > > > > > > > Grand prize is a trip for two to an Open Source event anywhere in the > world > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@li...> > > > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > > > > Build the coolest Linux based applications with Moblin SDK & win great > > > > > > > > prizes > > > > > > > > Grand prize is a trip for two to an Open Source event anywhere in the > world > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin- > contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@li...> > > > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > > > -- > > > > David Creasy > > > > Matrix Science > > > > 64 Baker Street > > > > London W1U 7GB, UK > > > > Tel: +44 (0)20 7486 1050 > > > > Fax: +44 (0)20 7224 1344 > > > > > > > > dc...@ma... <mailto:dc...@ma...> > > > > http://www.matrixscience.com > > > > > > > > Matrix Science Ltd. is registered in England and Wales > > > > Company number 3533898 > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > > > > Build the coolest Linux based applications with Moblin SDK & win great prizes > > > > Grand prize is a trip for two to an Open Source event anywhere in the world > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin- > contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@li...> > > > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > > > > Build the coolest Linux based applications with Moblin SDK & win great prizes > > > > Grand prize is a trip for two to an Open Source event anywhere in the world > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin- > contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@li...> > > > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > > Build the coolest Linux based applications with Moblin SDK & win great prizes > > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 |
|
From: Martin E. <mar...@ru...> - 2008-10-23 14:05:23
|
Thank you for the changes!
One remark: we run into problems with the composite uniqueness of
(spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines.
Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList;
there the same spectrum is (usually) referenced (with the same or another peptide sequences as
SpectrumIdentificationItems, but other scores).
We should drop that composite unique key.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 16, 2008 6:26 PM
An: psi...@li...
Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult - one SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique,
removed SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be
attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this,
and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more
molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential
peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in
MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want
to postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here unless anyone
disagrees?
David
--
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Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
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From: Jones, A. <And...@li...> - 2008-10-23 14:13:48
|
If we represent different search engines within the same document, we have separate SpectrumIdentificationLists. So the composite key would work if it is (SpectrumIdentificationList ID, spectrumID, SpectraData_ref) I think? Cheers Andy From: Martin Eisenacher [mailto:mar...@ru...] Sent: 23 October 2008 15:05 To: Jones, Andy Cc: psi...@li... Subject: AW: [Psidev-pi-dev] AnalysisXML PMF Example Thank you for the changes! One remark: we run into problems with the composite uniqueness of (spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines. Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList; there the same spectrum is (usually) referenced (with the same or another peptide sequences as SpectrumIdentificationItems, but other scores). We should drop that composite unique key… Bye Martin Von: Jones, Andy [mailto:And...@li...] Gesendet: Thursday, October 16, 2008 6:26 PM An: psi...@li... Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example New schema uploaded by SVN with changes agreed on the call: - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data) - Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification - Altered documentation for SpectrumIdentificationResult – one SpectrumIdentificationResult for one spectrum - Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique, removed SpectrumElement Andy From: Pierre-Alain Binz [mailto:pie...@is...] Sent: 16 October 2008 14:26 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 13:54 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: Hi David, You may be right that the parameter should be optionally anyway, but in this particular example is there not some score assigned to the peptide-spectrum identification? In the equivalent MS/MS example, we have: <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="62.72" /> <pf:cvParam accession="PI:00172" name="mascot:expectation value" cvRef="PSI-PI" value="0.000863428353297988" /> <pf:cvParam accession="PI:99999" name="mascot_rank" cvRef="PSI-PI" value="1" /> Are the same sort of scores not valid for PMF as well...? Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 12:29 To: psi...@li... Subject: [Psidev-pi-dev] AnalysisXML PMF Example Hi All, There's an example PMF file here: http://code.google.com/p/psi- pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? David -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
|
From: Martin E. <mar...@ru...> - 2008-10-23 14:45:56
|
Yes, that works for our example!
I will add this one row to the schema and commit.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 23, 2008 4:13 PM
An: Martin Eisenacher
Cc: psi...@li...
Betreff: RE: [Psidev-pi-dev] AnalysisXML PMF Example
If we represent different search engines within the same document, we have separate SpectrumIdentificationLists.
So the composite key would work if it is (SpectrumIdentificationList ID, spectrumID, SpectraData_ref) I think?
Cheers
Andy
From: Martin Eisenacher [mailto:mar...@ru...]
Sent: 23 October 2008 15:05
To: Jones, Andy
Cc: psi...@li...
Subject: AW: [Psidev-pi-dev] AnalysisXML PMF Example
Thank you for the changes!
One remark: we run into problems with the composite uniqueness of
(spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines.
Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList;
there the same spectrum is (usually) referenced (with the same or another peptide sequences as
SpectrumIdentificationItems, but other scores).
We should drop that composite unique key.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 16, 2008 6:26 PM
An: psi...@li...
Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult - one SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique,
removed SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be
attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this,
and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more
molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential
peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in
MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want
to postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here unless anyone
disagrees?
David
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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--
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Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
-------------------------------------------------------------------------
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Grand prize is a trip for two to an Open Source event anywhere in the world
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From: Martin E. <mar...@ru...> - 2008-10-23 14:51:06
|
Oops, is not as easy as adding one row, because the SpecList id is one level up.
Someone please help.
Von: Martin Eisenacher [mailto:mar...@ru...]
Gesendet: Thursday, October 23, 2008 4:46 PM
An: 'Jones, Andy'
Cc: 'psi...@li...'
Betreff: AW: [Psidev-pi-dev] AnalysisXML PMF Example
Yes, that works for our example!
I will add this one row to the schema and commit.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 23, 2008 4:13 PM
An: Martin Eisenacher
Cc: psi...@li...
Betreff: RE: [Psidev-pi-dev] AnalysisXML PMF Example
If we represent different search engines within the same document, we have separate SpectrumIdentificationLists.
So the composite key would work if it is (SpectrumIdentificationList ID, spectrumID, SpectraData_ref) I think?
Cheers
Andy
From: Martin Eisenacher [mailto:mar...@ru...]
Sent: 23 October 2008 15:05
To: Jones, Andy
Cc: psi...@li...
Subject: AW: [Psidev-pi-dev] AnalysisXML PMF Example
Thank you for the changes!
One remark: we run into problems with the composite uniqueness of
(spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines.
Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList;
there the same spectrum is (usually) referenced (with the same or another peptide sequences as
SpectrumIdentificationItems, but other scores).
We should drop that composite unique key.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 16, 2008 6:26 PM
An: psi...@li...
Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult - one SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique,
removed SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be
attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this,
and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more
molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential
peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in
MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want
to postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here unless anyone
disagrees?
David
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100 <http://moblin-contest.org/redirect.php?banner_id=100&url=/> &url=/
_______________________________________________
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-------------------------------------------------------------------------
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_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
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--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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